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In a recent printed piece, some scale distortion occurred. The piece has about 7 cm height and it was compressed about 4mm. Measurements revealed that lower layers were compressed and higher layers seem ok.

What could cause that behavior?

During that printing I could hear some clicks and I've noticed those clicks were originated from the platform because I could feel it touching on the platform. Can it be a malfunction?

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Well it could be the driver overheating but that usually causes your part to be taller, not shorter but here is an old post below - I would remove the bottom cover, tilt the printer and have a fan blowing some air on the circuitry and then start a new print. Just to see if that helps. If not then ignore this "hot z driver issue" below:

Hot feeder driver. I've seen a more recent problem in the forums (>=2015) where people's stepper drivers get too hot - this is mostly a problem with the Z axis but also with the feeder. The high temps means the driver appears to shut down for a well under a second - maybe there is a temp sensor built into the driver chip? The solution from Ultimaker is that they lowered all the currents to their stepper drivers in the newer firmware. Another solution is to remove the cover and use desk fan to get a tiny bit of air movement under there. TinkerMarlin lets you set the currents from the menu system or you can send a gcode to lower the current. Ultimaker lowered the default currents in July of 2015 from 1300ma to 1200ma for X,Y,Z but left extruder at 1250. Other people (I think the support team of a major reseller but I forget) recommend X,Y,Z go down to 1000mA.

M907 E1250

Above sets the extruder max current to the default - 1250mA. So try 900mA. This will only change until next power cycle so if you like your new value and want to save it use M500. You can just put these into an otherwise empty gcode file and "print" this and it will change. Or get tinkergnome marlin! You will wonder how you lived without it: https://github.com/TinkerGnome/Ultimaker2Marlin/releases

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Instead it might just be something is loose with the Z screw and/or Z nut. The Z screw might not be properly connected to the stepper and it may slip. I thought that was impossible but maybe? Or maybe the Z current is too weak?

I guess if it's not the heat issue above I would connect the printer to a PC through USB and install pronterface on that machine. I would then direct the bed to move up and down by 1mm, 10mm, and 100mm movements. I would measure how far it moved (maybe a type a ruler to the side of the machine near the bed? and also feel it. See if I could feel something strange. Pronterface is free and easy to use:

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Actually, I noticed that there occur vertical displacements of the platform while printing in the same layer. First a down silent displacement and immediately after a noisy displacement going up. Is it related to the referred hot z driver issue?

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I don't know why it would move the bed down and up unless you had one of the "hop" options enabled in cura. Check cura for that - cura has ability to search for a setting. But I doubt that is related.

Well if you suspect heat - try putting something heavy on the bed - around 5kg - maybe a brick or hand weight. Put it in the back of the bed after printing is started and see if your "scale distortion" gets worse or better. It should not make any difference.

PLEASE PLEASE PLEASE also post photos of your prints and maybe a video of the "two displacements on one layer" thing you are talking about.

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Designing for light-weight parts is becoming more important, and I’m a firm believer in the need to produce lighter weight, less over-engineered parts for the future. This is for sustainability reasons because we need to be using less raw materials and, in things like transportation, it impacts the energy usage of the product during it’s service life.